Update deprecated amici imports

pypesto/hierarchical/inner_calculator_collector.py

@@ -48,7 +48,7 @@
 try:
     import amici
     import petab
-    from amici.parameter_mapping import ParameterMapping
+    from amici.petab.parameter_mapping import ParameterMapping
 except ImportError:
     petab = None
     ParameterMapping = None
@@ -325,7 +325,7 @@ def __call__(
             Whether to use the FIM (if available) instead of the Hessian (if
             requested).
         """
-        import amici.parameter_mapping
+        from amici.petab.conditions import fill_in_parameters
 
         if mode == MODE_RES and any(
             data_type in self.data_types
@@ -403,7 +403,7 @@ def __call__(
         x_dct = copy.deepcopy(x_dct)
         x_dct.update(self.necessary_par_dummy_values)
         # fill in parameters
-        amici.parameter_mapping.fill_in_parameters(
+        fill_in_parameters(
             edatas=edatas,
             problem_parameters=x_dct,
             scaled_parameters=True,

pypesto/hierarchical/ordinal/calculator.py

@@ -32,7 +32,8 @@
 
 try:
     import amici
-    from amici.parameter_mapping import ParameterMapping
+    from amici.petab.conditions import fill_in_parameters
+    from amici.petab.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 
@@ -155,7 +156,7 @@ def __call__(
             x_dct = copy.deepcopy(x_dct)
 
             # fill in parameters
-            amici.parameter_mapping.fill_in_parameters(
+            fill_in_parameters(
                 edatas=edatas,
                 problem_parameters=x_dct,
                 scaled_parameters=True,

pypesto/hierarchical/ordinal/solver.py

@@ -37,7 +37,7 @@
 from .problem import OrdinalProblem
 
 try:
-    from amici.parameter_mapping import ParameterMapping
+    from amici.petab.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 

pypesto/hierarchical/relative/calculator.py

@@ -7,8 +7,8 @@
 
 try:
     import amici
-    import amici.parameter_mapping
-    from amici.parameter_mapping import ParameterMapping
+    from amici.petab.conditions import fill_in_parameters
+    from amici.petab.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 
@@ -296,7 +296,7 @@ def calculate_directly(
             amici_solver.setSensitivityOrder(sensi_order)
             x_dct.update(self.inner_problem.get_dummy_values(scaled=True))
             # fill in parameters
-            amici.parameter_mapping.fill_in_parameters(
+            fill_in_parameters(
                 edatas=edatas,
                 problem_parameters=x_dct,
                 scaled_parameters=True,

pypesto/hierarchical/relative/solver.py

@@ -27,7 +27,7 @@
 
 try:
     import amici
-    from amici.parameter_mapping import ParameterMapping
+    from amici.petab.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 

pypesto/hierarchical/semiquantitative/calculator.py

@@ -32,7 +32,8 @@
 
 try:
     import amici
-    from amici.parameter_mapping import ParameterMapping
+    from amici.petab.conditions import fill_in_parameters
+    from amici.petab.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 
@@ -154,7 +155,7 @@ def __call__(
             )
 
             # fill in parameters
-            amici.parameter_mapping.fill_in_parameters(
+            fill_in_parameters(
                 edatas=edatas,
                 problem_parameters=x_dct,
                 scaled_parameters=True,

pypesto/hierarchical/semiquantitative/solver.py

@@ -27,7 +27,7 @@
 from .problem import SemiquantProblem
 
 try:
-    from amici.parameter_mapping import ParameterMapping
+    from amici.petab.parameter_mapping import ParameterMapping
 except ImportError:
     pass
 

pypesto/objective/amici/amici_util.py

@@ -24,7 +24,7 @@
 if TYPE_CHECKING:
     try:
         import amici
-        from amici.parameter_mapping import (
+        from amici.petab.parameter_mapping import (
             ParameterMapping,
             ParameterMappingForCondition,
         )
@@ -124,23 +124,25 @@ def create_identity_parameter_mapping(
     both in preequilibration and simulation, are assumed to be provided
     correctly in model or edatas already.
     """
-    import amici.parameter_mapping
+    from amici.petab.parameter_mapping import (
+        ParameterMapping,
+        ParameterMappingForCondition,
+        amici_to_petab_scale,
+    )
 
     x_ids = list(amici_model.getParameterIds())
     x_scales = list(amici_model.getParameterScale())
-    parameter_mapping = amici.parameter_mapping.ParameterMapping()
+    parameter_mapping = ParameterMapping()
     for _ in range(n_conditions):
         condition_map_sim_var = {x_id: x_id for x_id in x_ids}
         condition_scale_map_sim_var = {
-            x_id: amici.parameter_mapping.amici_to_petab_scale(x_scale)
+            x_id: amici_to_petab_scale(x_scale)
             for x_id, x_scale in zip(x_ids, x_scales)
         }
         # assumes fixed parameters are filled in already
-        mapping_for_condition = (
-            amici.parameter_mapping.ParameterMappingForCondition(
-                map_sim_var=condition_map_sim_var,
-                scale_map_sim_var=condition_scale_map_sim_var,
-            )
+        mapping_for_condition = ParameterMappingForCondition(
+            map_sim_var=condition_map_sim_var,
+            scale_map_sim_var=condition_scale_map_sim_var,
         )
 
         parameter_mapping.append(mapping_for_condition)

pypesto/visualize/model_fit.py

@@ -14,6 +14,7 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import petab
+from amici.petab.conditions import fill_in_parameters
 from amici.petab.simulations import rdatas_to_simulation_df
 from petab.visualize import plot_problem
 
@@ -269,7 +270,7 @@ def _get_simulation_rdatas(
         for j in range(len(edatas)):
             edatas[j].setTimepoints(simulation_timepoints)
 
-        amici.parameter_mapping.fill_in_parameters(
+        fill_in_parameters(
             edatas=edatas,
             problem_parameters=x_dct,
             scaled_parameters=True,

pypesto/visualize/ordinal_categories.py

@@ -9,6 +9,7 @@
 
 try:
     import amici
+    from amici.petab.conditions import fill_in_parameters
     from petab.C import OBSERVABLE_ID
 
     from ..hierarchical.ordinal.calculator import OrdinalCalculator
@@ -86,7 +87,7 @@ def plot_categories_from_pypesto_result(
     n_threads = pypesto_result.problem.objective.n_threads
 
     # Fill in the parameters.
-    amici.parameter_mapping.fill_in_parameters(
+    fill_in_parameters(
         edatas=edatas,
         problem_parameters=x_dct,
         scaled_parameters=True,

pypesto/visualize/spline_approximation.py

@@ -23,6 +23,7 @@
 
 try:
     import amici
+    from amici.petab.conditions import fill_in_parameters
 
     from ..hierarchical import InnerCalculatorCollector
     from ..hierarchical.semiquantitative.calculator import SemiquantCalculator
@@ -105,7 +106,7 @@ def plot_splines_from_pypesto_result(
     observable_ids = amici_model.getObservableIds()
 
     # Fill in the parameters.
-    amici.parameter_mapping.fill_in_parameters(
+    fill_in_parameters(
         edatas=edatas,
         problem_parameters=x_dct,
         scaled_parameters=True,
@@ -379,7 +380,7 @@ def _add_spline_mapped_simulations_to_model_fit(
     n_threads = pypesto_problem.objective.n_threads
 
     # Fill in the parameters.
-    amici.parameter_mapping.fill_in_parameters(
+    fill_in_parameters(
         edatas=edatas,
         problem_parameters=x_dct,
         scaled_parameters=True,
@@ -528,7 +529,7 @@ def _obtain_regularization_for_start(
     n_threads = pypesto_result.problem.objective.n_threads
 
     # Fill in the parameters.
-    amici.parameter_mapping.fill_in_parameters(
+    fill_in_parameters(
         edatas=edatas,
         problem_parameters=x_dct,
         scaled_parameters=True,